Tuesday, June 30, 2009

Genes, Phylogeny, and Orangutans

Jeffrey H. Schwartz is well known to talk.origins veterans because we discussed his book (Sudden Origins: Fossils, Genes, and the Emergence of Species) back in 1999. Schwartz tried to make the case for a "groundbreaking and radical new theory of evolution." This "theory" was based on the idea that new species spring into existence very quickly when a mutation in a homeobox (HOZ) gene arises in a population. It's a "theory" of saltation but it's based on such a flawed understanding of genetics that you really have to read to book to see just how bad it is. Sudden Origins is a leading candidate for the worst science book ever published.

In case you want to see a shorter version, the basic idea is explained in Schwartz (1999).

Over the years, Schwartz has published many other ideas that are controversial. Lately he has been pushing the concept that molecular phylogenies are unreliable. In part this is because he is opposed to gradual change as documented in the record of the genes. He thinks that real evolution takes place when alterations of regulatory genes result in major new phenotypes. Thus, the best way to discover the history of life is to examine anatomical homologies and differences.

But part of the problem lies in Jeffrey Schwartz's idiosyncratic understanding of genetics and molecular biology. When you put these together, this is what you get in Schwartz (2009).
This having been said, systematics and evolutionary biology need not remain estranged. Developmental biology increasingly makes clear that organismal change (and by extension, evolution), is not how it was imagined when the synthesis emerged (see reviews in Schwartz 1999, 2009b; Maresca and Schwartz 2006). Further, because of the interrelation between, e.g., the physical properties of cells, signaling pathways, epigenetic effects and development and consequently the origination of form, the false dichotomy of ‘‘molecules versus morphology’’ that resulted in the 1980s from the dethroning of morphology by the hegemony of molecular analyses is no longer tenable (Schwartz 2009a). Indeed, the undeniable hierarchical continuum from the molecular through the morphological, firmly centralizes morphology (as understood via development) in systematic endeavors (Schwartz 2009a).
Grahan and Schwartz (2009) have just published a paper in which they claim that orangutans are more closely related to humans that are chimpanzees. According to them, the molecular data is not reliable. They claim that detailed morphological comparisons show that orangutans are our closest ancestor.

John Hawks asks the question "Are orangutans our closest living relatives?" and he comes up with the best possible answer to scientists with a well-known history of promoting "unusual" positions on evolution.

It's a lesson that New Scientist should have learned. They devote several pages to the Grahan and Schwartz paper thereby giving it much more publicity than it deserves [Could the orang-utan be our closest relative?].1 The article is written by Graham Lawton who you might remember from the "Tree of Life" episode [see: Explaining the New Scientist Cover]. The editors of New Scientist knew full well that their decision would be controversial so they took a proactive position by writing a short editorial [In praise of scientific heresy ].
If its claims are so outlandish, should the research even have been published? Some scientists would clearly have preferred it if the paper had never seen the light of day, and question the judgement of the journal.

That is territory we should tread with care. Ideas that mainstream opinion "knows" to be wrong occasionally turn out to be right. The insights of Galileo, Stan Prusiner - who discovered prions - and many others were once denounced as heresy. And even those that are wrong can be valuable.

Science proceeds by questioning its own assumptions and regarding every "fact" as provisional, so alternative hypotheses should be given an airing, if only to reaffirm the strength of the orthodoxy. Science that pulls up the drawbridge on new ideas risks becoming sterile. The journal recognised that and should be applauded for its decision to disseminate this challenging paper.
There's some truth here, but only some. You can't use Stanley Prusiner as an excuse to publish every crazy idea that comes along. Some ideas really are crazy—they are not revolutions in disguise. The plain fact is that Jeffrey H. Schwartz has already had his chance to make his case and he has not been successful. How many chances does he get before we draw the obvious conclusion?

1. The article was two pages long and the editorial was much less than one page. This may not qualify as "several" pages by some definitions.

[Photo Credit: Daily Mail]

Grehan, J.R. and Schwartz, J.H. (2009) Evolution of the second orangutan: phylogeny and biogeography of hominid origins. Journal of Biogeography, published online June 22. 2009. [doi:10.1111/j.1365-2699.2009.02141.x]

Schwartz, J.H. (1999) Homeobox genes, fossils, and the origin of species. Anat Rec. 15:15-31. [PubMed]

Schwartz, J.H. (2009) Reflections on Systematics and Phylogenetic
Reconstruction. Acta Biotheor 57:295–305 [doi: 10.1007/s10441-009-9078-9]

What Can Scientists Do to Help Science Journalism?

This week's issue of Nature has a number of articles devoted to science journalism. Their publication coincides with the 6th World Conference of Science Journalists in London, UK.

One of the articles is an editorial, Cheerleader or watchdog?, about what scientists can do to help science journalism.
Scientists can do little to stem this bloodletting. But whatever they can do to engage with those caught up in it, and ensure that questioning and informed science journalism persists, will be worthwhile. If there is to be a transition to new — perhaps philanthropic — business models for in-depth reporting or new types of analytical media, science journalism will integrate into them all the better if scientists are taking an active interest in its health. And if the future of the media truly is a dire landscape of top-100 lists, shouting heads and minimal attention span, then such efforts might at least defer the grim end.

Even amid the turmoil, however, scientists can help ensure that reporting about science continues to be both informed and accurate.
I agree that scientists should work on trying to make science reporting more accurate. So far, we haven't been too successful.

But there's another important contribution we can make. We can help clean up our own act so that less bad science is published. This will not only make science better, it will have the spin-off effect of making life easier for science journalists. At the very least, we should make sure that press releases coming from our institutions are accurate. Every scientists should have to stand behind and endorse the press releases from their supporting institution. Let's take responsibility.

Also, wouldn't it be nice if most of the papers published in the scientific literature were careful to put their work in the proper perspective? Wouldn't it be nice if scientists themselves stopped exaggerating their contributions and stopped making outrageous claims? Science journalists have not done a good job of sifting the wheat from the chaff, in spite of what they think. They are far from blameless but scientists carry a bigger share of the blame for the sorry state of science literacy.

Campus Excitement

There's usually something exciting happening on the University of Toronto campus during the summer.

It's a popular location for shooting movies and TV shows and you never know what you'll find on any given day. This is the scene that greeted me today when I emerged from the subway station. It took a few seconds to realize that I wasn't in the middle of a real emergency.

Last week the front campus was the scene of a bank truck robbery in Germany, just in front of a sidewalk café. I wish they'd left the outdoor tables and umbrellas and kept serving the wine and food.

Monday, June 29, 2009

Monday's Molecule #127


Today's molecule stinks.1 You have to identify it by giving me the common name and the IUPAC name.

There's only one Nobel Laureate whose name is linked to this molecule. The Laureate was responsible for determining its structure.

The first person to identify the molecule and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, Bill Chaney of the University of Nebraska and Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

Bill Chaney has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

1. Opinions may vary.

Sunday, June 28, 2009

Grandpa Burger

When I was (much) younger I used to order the Teen Burger when we went to the A&W. Even after I stopped being a teenager I still got the Teen Burger 'cause I wasn't really eligible for any of the others.

While we were living in Europe there were no A&W's in our part of the world so I didn't have a problem choosing what to order. By the time we returned to Canada, Jane had been born and I could order the Papa Burger without feeling guilty.1

Here I am at the the A&W yesterday, trying out the Grandpa Burger. Technically, I won't be officially eligible for the Grandpa Burger until next January. Coincidentally, that's when my daughter Jane and her husband Michael will be able to buy the Mama and Papa Burgers.

1. I sometimes cheated and ordered the teenburger anyway.

[Hat Tip: A&W Grandpa Burger commercial.]

Saturday, June 27, 2009

Everything You Wanted to Know About Canada but Were Afraid to Ask

The Canadian system of government can be a little difficult to understand and recent political events in Canada don't make it any easier. Here's a brief and dumbed-down lesson on Canadian politics. It's intended mostly for Canadians but foreigners might also find it helpful.

Thanks to Greg Laden most readers on his blog are now much more knowledgeable about Canada than most Canadians.

The Great, Profound, and Valuable Works of Evolutionary Psychology

A few weeks ago I was having an email discussion about evolutionary psychology with Gad Saad. Readers may recall an earlier posting about Gad's work on the correlation between the length of one's fingers and the kinds of things one likes to buy in a store [Psychology and Finger Length].

One of my criticisms of evolutionary psychology is that its proponents don't usually seem to have a good handle on modern evolutionary biology. Gad argues that, while this may be true for some evolutionary psychologists, it's not a widespread problem. He, for example, considers himself to be very knowledgeable about evolution. His undergraduate degree is in Mathematics and Computer Science. He then went on to obtain an MBA, an MS in Management, and finally a PhD in Marketing [Gad Saad].

He is currently an Associate Professor in the Marketing Department at Concordia University, Montreal, Canada. But over the years he has learned a great deal about evolution and in 2008 he was appointed to the "Concordia University Research Chair in Evolutionary Behavioral Sciences and Darwinian Consumption." Gad explained to me that this appointment was recommended by several experienced evolutionary biologists.

We weren't making much progress in our email discussions. It seemed that we had been reading different accounts of evolutionary theory because we couldn't agree on some basic concepts. Nevertheless, Gad advanced a number of vigorous defenses of evolutionary psychology including the following point that I reproduce from our email exchange with his permission. (Actually, he gave me permission to post his list of "great, profound, and valuable works" but not the actual paragraph where he made the claim. I posted the actual claim because it differs from what Gad said in the comment to my earlier posting.)
You are indeed correct that evolutionary psychology has at times succumbed to the allure of just-so storytelling. That said, it is unfair (and frankly dishonest of you) to place all evolutionary behavioral scientists under the negative umbrella that you repeatedly do. Evolutionary psychologists produce great, profound, and valuable works, and at times can produce weaker works with tenuous conclusions. This holds true of biochemists as well. Physicists disagree as to whether String Theory is valid or not. Should we equally view physicists as providers of shoddy and controversial work?
I was intrigued by the claim that evolutionary psychologists have produced "great, profound, and valuable works" and I asked for examples. He supplied them but around that time I got distracted by real life and didn't follow up on our email exchanges.

Now Gad has posted his list in the comments to yesterday's posting on Why Evolutionary Psychology Is False.

I think it deserves wider coverage so here, without comment, is Gad Saad's list of the great, profound, and valuable works of evolutionary psychology. This is the best of the best by one of the leading experts in the field. I think we can get a good sense of the overall quality of the discipline by examining the list.
  1. Women alter their preferences for the facial features of men as a function of where they are in their menstrual cycles. When maximally fertile, they prefer men possessing markers of high testosterone.
  2. Babies display an immediate instinctual preference for symmetric faces (at an age that precedes the capacity for socialization).
  3. Children who suffer from congenital adrenal hyperplasia display a reversal in their toy preferences. Furthermore, using inter-species comparisons, vervet monkeys display the same sex-specific patterns of play/toy preferences as human infants. This suggests that contrary to the argument made by social constructivists, play has an evolved biological basis.
  4. Individuals who score high on an empathy scale are more likely to succumb to the contagion effects of yawning. This is indicative that this particular contagion might be linked to mimicry and/or Theory of Mind.
  5. How provocatively a woman dresses is highly correlated to her menstrual cycle (a form of sexual signaling found across countless Mammalian species).
  6. Culinary traditions are adaptations to local niches. For example, the extent to which a culture utilizes meat versus vegetables, spices, or salt is a cultural adaptation (this is what behavioral ecologists study).
  7. Maternal grandmothers and paternal grandfathers invest the most and the least respectively in their grandchildren. Whereas all four grandparents have a genetic relatedness coefficient of 0.25 with their grandchildren, they do not all carry the same level of "parental uncertainty." In the case of maternal grandmothers, there is no uncertainty whereas in the case of the paternal grandfather, there are two sources of uncertainty. This last fact drives the differential pattern of investment in the grandchildren.
  8. Good male dancers are symmetric (paper published in Nature). One would expect that some behavioral traits might correlate with phenotypic quality as honest signals of an individual's desirability on the mating market.
  9. Self-preference for perfumes is linked to one's immunogenetic profile (Major Histocompatibility Complex).
  10. When a baby is born, most family members (especially those of the mother) are likely to state that the baby looks like the father. This phenomenon is found in countless cultures despite the fact that it is objectively impossible to make such a claim of resemblance. The reason for this universally found cultural tradition lies in the need to assuage the fears of paternity uncertainty.
  11. Environmental stressors (e.g., father absence) and the onset of menarche (first menses) have been shown to be highly linked. In numerous species, the likelihood of a female becoming reproductively viable is affected by environmental contingencies.
  12. Women are less receptive to mandatory hospital DNA paternity testing (for obvious reasons). In other words, their willingness to adopt a new product/service is fully driven by an evolutionary-based calculus.
  13. Women can smell the most symmetric men. In other words, women have the capacity to identify men who possess the best phenotypic quality simply via their nose. This is what I have referred to as sensorial convergence.
  14. Using fMRI, the exposure to ecologically-relevant stimuli (e.g., beautiful faces) yields distinct neural activation patterns in men and women.
  15. In choosing a mate, humans tend to prefer the smell of others that are maximally dissimilar to them along the MHC. This ensures that offspring possess a greater "defensive coverage" in terms of their immunological system.

Friday, June 26, 2009

Swine Flu Is Caused by French Fries

According the a report from Russia, the current swine flue pandemic is caused by genetically modified potatoes that are sold as French Fries in many Western industrialized nations [Russian Scientists Warn Of Genetically Modified Fast Food Link To Pandemic Flu].
Scientists from Russia’s Ministry of Health are warning in a secret report to Prime Minister Putin that they have discovered a ‘critical link’ between the H1N1 influenza (Swine Flu) virus and genetically modified amylopectin potatoes that are consumed in massive quantities nearly exclusively by Westerners and sold in fast food restaurants as French Fries.

According to these reports, the protease enzyme genetically modified in the potatoes being sold through Western fast food restaurants as French Fries to protect against Potato virus X causes an “explosive” replication of the H1N1 influenza virus by increasing the acidic conditions of the endosome and causing the hemagglutinin protein to rapidly fuse the viral envelope with the vacuole's membrane, then causing the M2 ion channel to allow protons to move through the viral envelope and acidify the core of the virus, which causes the core to dissemble and release the H1N1’s RNA and core proteins into the hosts cells.

Evidence confirming these dire findings by top Russian scientists is also supported by the World Health Organization who in their reporting on the current Influenza Pandemic, clearly shows that the H1N1 virus is nearly totally confined to those Western Nations allowing their citizens to consume these genetically modified potatoes, and which include: The United States with over 17,000 cases being reported with 45 deaths; Canada with 2,978 cases; the United Kingdom with 1,226 cases; and Australia with 1,823 cases.
This is very troubling. I'd like to be an accommodationist and pretend that the Russian kooks scientists are every bit as good as real scientists in other countries. On the other hand, my scientific instincts lead me to postulate that the claim is not very scientific and should be assigned to the urban legend category.

I'm in a quandary over whether I should believe this or not. We need the Russians as allies but we also need the French. Seems like one of them is going to be offended.

The Glory for Christ Football League

Normally I don't like piling on and I don't like making fun of spelling errors (because I make so many myself). But here's a photograph from the New York Times that every blogger is reproducing and I just can't help myself.

The New York Times ran an article on football teams for home schooled children and this photo appears on their website under the caption ...
The Glory for Christ Football League in Georgia grew out of a desire to provide an option for young men who are home-schooled but cannot play in local football leagues.

It's pretty obvious that "acedemics" and "atheletics" are not the top priorities of these homeschoolers but who knew they were so far down the list?

Why Evolutionary Psychology Is False

I haven't got time to review the recent publications on evolutionary psychology. The good news is that the popular press is finally waking up to the fact that the entire field is suspect. It sure took them long enough.

Read a summary on Why Evolution Is True: Genetic determinism? Not so fast.

Lawrence Krauss on Science vs Religion

Lawrence Krauss was recently asked to participate in a debate about science and religion. Ken Miller and another Roman Catholic scientist were there. Miller argued the case for compatibility and Krauss defended the atheist position. Here's how Krauss describes some of the debate in an article entitled God and Science Don't Mix.
Faced with the remarkable success of science to explain the workings of the physical world, many, indeed probably most, scientists understandably react as Haldane did. Namely, they extrapolate the atheism of science to a more general atheism.

While such a leap may not be unimpeachable it is certainly rational, as Mr. McGinn pointed out at the World Science Festival. Though the scientific process may be compatible with the vague idea of some relaxed deity who merely established the universe and let it proceed from there, it is in fact rationally incompatible with the detailed tenets of most of the world's organized religions. As Sam Harris recently wrote in a letter responding to the Nature editorial that called him an "atheist absolutist," a "reconciliation between science and Christianity would mean squaring physics, chemistry, biology, and a basic understanding of probabilistic reasoning with a raft of patently ridiculous, Iron Age convictions."

When I confronted my two Catholic colleagues on the panel with the apparent miracle of the virgin birth and asked how they could reconcile this with basic biology, I was ultimately told that perhaps this biblical claim merely meant to emphasize what an important event the birth was. Neither came to the explicit defense of what is undeniably one of the central tenets of Catholic theology.
This is the problem. Whenever you encounter a religious person who claims that there's no conflict between their religious beliefs and science, you have every right to engage in a discussion about the specific beliefs that they hold.

Do they believe in miracles? In my experience, religious scientists tend to avoid answering such direct questions just like they avoid answering questions about the efficacy of prayer, the existence of a soul, and life after death. I wonder why they won't answer these questions?

Thursday, June 25, 2009

John Wilkins Is an Asportist

Some questions are really very simple in spite of the fact that people want to make them complicated. When I ask you, "Do you believe in God?" it really doesn't require a lot of thought for most people. True, there might be a few people who want more clarification about the meaning of God but those people are the exceptions. Usually you can get a response by asking, "Are you a theist?"

There are only two possible answers to the second question. If the answer is "yes" then you are a theist. If the answer is "no" then you are not a theist. Most of the world can be conveniently divided into two groups: theists and non-theists. The others, those who answer "I don't know," aren't worth the bother.

We have a word for those who are non-theists. They are called atheists by my definition of the word. I use the word "atheist" in the same sense as any other word that begins with "a" and means "not." As Antony Flew puts it, the word atheist has the same connotation as "amoral," "atypical," and "asymmetrical." It means that you are not a theist. I'm also an athoothfairyist and an asantaclausian.

John Wilkins disagrees. He thinks the word atheist should be reserved for the strong belief that gods do not exist. When used in that sense, he would argue that he is not a theist and he does not actively deny the existence of gods. He is an agnostic. John divides the world into two camps—those who have a position on the existence or non-existence of god and those who don't. The latter group is the agnostics and he is one.

That's fine by me as long as John makes his definitions clear and he doesn't try to impose his definition of atheist on the rest of us. It would be wrong of John to call me an atheist using his definition so he better be careful. He would have to include me among the agnostics if he is being consistent. He'd also have to include Richard Dawkins. As a matter of fact, John might find it difficult to find anyone who is a true atheist by his definition.

I will try and respect John's wishes and refer to him as an agnostic who doesn't believe in god but doesn't advocate the nonexistence of gods as a philosophical position. However, I don't think I can go along with him in all cases ...
So, to summarise, when an atheist says to me I am an atheist because I lack a view, I am minded to reply, “I am also an asportist” for failing to have a team in any sport that I support. It makes about as much sense.
I'm sorry, John. I'll respect your (strange) opinion and not call you an atheist, but you really are an asportist!

Religion and the Templeton Foundation

From Jesus and Mo.

Blogging about Scientific Meetings

The question is whether it is legitimate for bloggers to report on what goes on at scientific conferences and meetings. I've done it several times and I never thought there was a problem.

Well, apparently some people disagree. Read about it in the latest issue of Nature: Science journalism: Breaking the convention?.
Blogs and Twitter are opening up meetings to those not actually there. Does that mean too much access to science in the raw, asks Geoff Brumfiel.
Next month I'm going to a meeting on "The Tree of Life." I intend to let you all know what goes on at that meeting but it shouldn't be a problem since the participants know what I'm doing and I won't be the only blogger.

There was a time, forty years ago, when some scientific meetings were very closed affairs and scientists could talk openly and frankly about what they were doing without fearing that it would be widely disseminated to non-insiders. There are still a few meetings like that but the vast majority are not.

Tuesday, June 23, 2009

Scientists Are no Different from Anyone Else

I admire Stephen Jay Gould for many reasons but his honesty ranks right up there near the top of the list.

Gould never pretended that individual scientists could be completely objective. He always said that they are no different than other people who have biases and prejudices. The special attributes of a scientist are that they recognize their biases and struggle to not let them influence their science.

He wrote a review of "Not in Our Genes: Biology, Idealogy and Human Nature" - a book by Richard Lewnotin, Steven Rose, and Leon J. Kamin, The review was later published in "An Urchin in the Storm."

In that review he acknowledged that he shared many of the opinions of the authors. He also wrote ...
... we scientists are no different from anyone else. We are passionate human beings, enmeshed in a web of personal and social circumstances. Our field does recognize canons of procedure designed to give nature the long shot of asserting herself in the face of such biases, but unless scientists understand their hopes and engage in vigorous self-scrutiny, they will not be able to sort out unacknowledged preference from nature's weak and imperfect message.
The problem in scientific discourse is not the background of the scientist but the strength and logic of the scientific arguments. It may be useful to see *why* certain scientists adopt certain positions at a particular point in time but that explains the history of an idea and not its correctness.
Leftist scientists are more likely to combat biological determinism just as rightests tend to favor this quintessential justification of the statu quo as intractable biology; the correlations are not accidental. But let us not be so disrespectful of thought that we dismiss the logic of arguments as nothing but an inevitable reflection of biases—a confusion of context of discovery whith context of justification.
Gould often laid his cards on the table when he confessed to his background. Whether it was baseball, a love of history, or a preference for New York, these were part of his personality and sometimes they crept into his science.

But honesty is not always the best policy. If you are honest enough to admit to prejudices and biases—even while you fight to suppress them—you aren't necessarily going to be admired. Especially if your opponents don't reveal their biases and pretend to be completely objective.

By drawing attention to the fact that scientists are no different than anyone else, Gould handed his enemies a weapon that could be used against him. How many of you have heard the charge that Gould is a Marxist, or (gasp!) a Liberal, and that's why he advocated Punctuated Equilibria? This is usually meant to discredit Gould because he revealed his background. Other scientists, who aren't so open, are given a free pass.

This is why you see a book about Gould and his politics but not a book about the politics of some of his opponents.

Monday, June 22, 2009

The Voyage That Shook the World

Watch the trailers and visit the website. Is this a film that promotes evolution?

No, it isn't [Creationists defend Darwin film].
Phil Bell, CEO of Creation Ministries UK, acknoweged that his organisation established a "front company" called Fathom Media, because they were concerned that experts such as Peter Bowler would not agree to take part in the film if they realised it was an "overtly Creationist" production. "At the end of the day," he said, "[when] people see 'Creationist', instantly the shutters go up and that would have shut us off from talking to the sort of experts, such as Professor Bowler, that we wanted to get to."

Grey hair may be protecting us from cancer

Another article from New Scientist documenting the slow decline of that journal into a typical supermarket rag [Grey hair may be protecting us from cancer ].
GREY hair may be unwelcome, but the processes that produce it are now better understood and could be protecting us from cancer.
First off, I want to make it clear that many of us with grey hair do not find it "unwelcome" in spite of societal pressures to make us feel embarrassed.

Second, here's the actual paper and abstract [doi:10.1016/j.cell.2009.03.037].

Inomata, K., Aoto, T., Binh, N.T., Okamoto, N., Tanimura, S., Wakayama, T., Iseki, S., Hara, E., Masunaga, T., Shimizu, H., and Nishimura, E.K. (2009) Genotoxic Stress Abrogates Renewal of Melanocyte Stem Cells by Triggering Their Differentiation. Cell 137: 1088-1099.
Somatic stem cell depletion due to the accumulation of DNA damage has been implicated in the appearance of aging-related phenotypes. Hair graying, a typical sign of aging in mammals, is caused by the incomplete maintenance of melanocyte stem cells (MSCs) with age. Here, we report that irreparable DNA damage, as caused by ionizing radiation, abrogates renewal of MSCs in mice. Surprisingly, the DNA-damage response triggers MSC differentiation into mature melanocytes in the niche, rather than inducing their apoptosis or senescence. The resulting MSC depletion leads to irreversible hair graying. Furthermore, deficiency of Ataxia-telangiectasia mutated (ATM), a central transducer kinase of the DNA-damage response, sensitizes MSCs to ectopic differentiation, demonstrating that the kinase protects MSCs from their premature differentiation by functioning as a “stemness checkpoint” to maintain the stem cell quality and quantity.
The idea is that DNA damage causes stem cells to differentiate into melanocytes that eventually die. Since there are fewer stem cells there will be fewer melanocytes produced over time and hair becomes grey. The fact that damaged stem cells undergo terminal differentiation instead of remaining as stem cells means that they are probably less likely to serve as the progenitors of a cancerous cell line.

Whether this has any real effect on protecting us from cancer is an open question. I doubt it very much but it's an easy hypothesis to test. Is it true that people with grey hair develop fewer cancers than people of the same age with darker hair?

Taxonomic Inflation

The number of new species discovered is growing every year, although we often hear more about threatened extinctions. In many cases this is because of new observations leading to the identification of new species. For the most part, these are not entirely new organisms—they are species that are closely related to existing species.

Given the ongoing battles between lumpers and splitters in the taxonomic community, one wonders whether the discovery of new species isn't just due to the elevation of varieties to the level of species. For example, there are many varieties of giraffe and some people propose that the current species, Giraffa camelopardalis, should be split into several species. This depends on your definition of species.

Christopher Taylor of Catalogue of Organisms reviews a recent paper that addresses the problem [Keeping an Eye on Inflation]. Turns out that the recent redefinition of species doesn't correlate with the increase in splitting so that doesn't seem to explain taxonomic inflation.

Unfortunately Chris doesn't answer the most important questions.
  • Is it true that God has an inordinate fondness for beetles or is it just overzealous insect taxonomists?

  • If you split G. camelopardalis then why not split Homo sapiens as well?

Sunday, June 21, 2009

Signature in the Cell

Denyse O'Leary can hardly contain herself 'cause Stephen Meyer's book is about to go on sale.

In case you can't wait, there's a Signature in the Cell website that explains the significance of this momentous event.
The foundations of scientific materialism are in the process of crumbling. In Signature in the Cell, philosopher of science Stephen C. Meyer shows how the digital code in DNA points powerfully to a designing intelligence behind the origin of life. The book will be published on June 23 by HarperOne.

Unlike previous arguments for intelligent design, Signature in the Cell presents a radical and comprehensive new case, revealing the evidence not merely of individual features of biological complexity but rather of a fundamental constituent of the universe: information. That evidence has been mounting exponentially in recent years, known to scientists in specialized fields but largely hidden from public view. A Cambridge University-trained theorist and researcher, director of the Discovery Institute’s Center for Science and Culture, Dr. Meyer is the first to bring the relevant data together into a powerful demonstration of the intelligence that stands outside nature and directs the path life has taken.


As a philosopher and a scientist himself, having worked in the field of geophysics for Atlantic Richfield, Meyer is able to step back from the fray of competing views about Darwinian theory and offer a searching, compelling investigation of life’s beginning.

Education and Science vs. Religion

As far as I'm concerned, the proper teaching of science involves explaining that it is a legitimate and powerful way of knowing based on evidence and rationalism. The scientific way of knowing conflicts with the vast majority of religious beliefs. In other words, the proper teaching of science is a threat to almost all religions and, in that sense, it encourages skepticism at least, and non-belief at best.

In most countries that fact isn't a problem but in the USA there's a problem. If the proper teaching of science promotes a "religious" point of view, namely atheism, then science can't be taught in public schools. It's fun to watch the contortions that many atheists have to go through in order to escape the obvious conclusion.

Andrew Brown (not an American, I might add) points out the problem [on being told by PZ ...]. I agree with him just as I agreed that Michael Ruse was making a valid point at the recent Center for Inquiry conference [Wherein Michael Ruse Avoids My Questions].

Jerry Coyne tries to get around the problem by concentrating on the teaching of evolution (just the scientific truth) and not "science" [Andrew Brown makes another dumb argument for accommodationism]. I think this is disengenuous but I do agree with Coyne that Andrew makes a silly case for accommodationism.

Coyne says,
Actually, we teach evolution because it’s a wonderful subject, explains a lot about the world, and happens to be true. And yes, it’s likely that teaching evolution probably promotes a critical examination of religious beliefs that may lead to rejecting faith. But teaching geology, physics, or astronomy does that, too.
This seems to contradict his main argument since it implies that teaching science does, indeed, lead to rejecting religious beliefs. But, wait a minute, he goes on to say that ..
In fact, education in general leads to the rejection of faith. (Statistics show that the more education one has, the less likely one is to be religious.) Should we then worry about teaching physics, astronomy, or indeed, allowing people access to higher education, because those “promote” atheism?
No, we shouldn't "worry" about that but it would be foolish to deny it. The essence of the scientific way of knowing is evidence, rationalism, and also one-mindedness and skepticism. We need to teach that to our children. To deny that this is inimical to faith-based ways of knowing is to deny the obvious.
Should we constantly be looking over our shoulders because the courts may catch onto this?
Maybe you should, if you live in America. The evolutionist side in America has put a high value on winning court cases based on rather arcane legal arguments—who, besides lawyers, cares about the Lemon test? If the bad guys decide to fight back in the courts by challenging the teaching of proper science then watch out. I've heard there are a lot of lawyers in America.

Speaking of lawyers, John Pieret has an opinion on this subject [Science, Philosophy and Law].
Teach only the science and the "problem" evaporates. Any tendency to reject faith because of the teaching of the science is what church and state scholar Kent Greenawalt has called "spillover effects," which do not render the teaching unconstitutional because they are not a "primary effect" of it.
If I understand him correctly, the teaching of Intelligent Design Creationism is unconstitutional because its "primary effect" is to promote religion. The teaching of evidence based rationalism (i.e. scientific reasoning) has as its primary purpose the destruction of superstitious beliefs but the fact that this includes religion is just a "spillover effect."

Wouldn't it be ironic if American courts ruled that it is unconstitutional to teach children how to think?

Common Sense, Rationalism, and other Points of Views

Steven Pinker is an evolutionary psychologist. In this debate he defends that point of view. The other participants in the debate don't agree and I think they make a lot of sense.

You can also listen to Steve Jones defend the idea that human evolution has stopped. In that discussion you'll probably notice that random genetic drift isn't mentioned. I get the impression that most of the time none of the participants think about anything other than natural selection when they're discussing evolution. (But see part 5, where "random variation" is briefly mentioned.) However, I'm sure they'll deny that they are adaptationists when challenged. I'm sure they'll swear up and down that they know all about the other mechanisms of evolution.

Bora Zivkovic Writes About Journalism

Bora Zivkovic of A Blog Around the Clock has long been interested in the role of journalists—especially science journalists—in our society. He writes about the legitimacy of quotations in The Ethics of the Quote.

At the risk of incurring his wrath for quote mining, I give you one of the most important and controversial ideas in his posting.
Even when asked, journalists openly state that their role is not to find the truth, but to register the spectrum of opinions out there. That is stenography at best (not even that, as some opinions are never registered, including some very valid opinions), not journalism.

But that is absolutely NOT what the audience expects. Audience is already aware of the spectrum of opinions out there. They look for you to tell them exactly which one of those opinions is correct, and which ones are bunk. But you never deliver. Which is why people are mad, and the press has an extremely low ranking in popular opinion on trustworthiness.

If you disagree with the above paragraph, think why that is so? Did you hear it from your editors and colleagues? If so, they are dead wrong. If you learned it in J-school, your professors were dead wrong. Wrong, wrong, wrong, wrong, wrong, wrong!!!

Now think again.

Is everything you ever learned in a professional setting about the role of journalism wrong? Could be. Time for deep introspection.
I agree with Boris when he says that journalists don't deliver, however I disagree with him slightly about what they think they are doing. Many journalists think their role is just what Boris says it should be. They believe that journalists should be able to explain which ideas are wrong and which ones are correct. Many science journalists claim to be able to do this. They claim that they don't just report the opinions of scientists who disagree but provide "value added" by figuring out which ones are correct.

If that's what they're trying to do then they don't do a very good job in the fields that I'm familiar with.

Friday, June 19, 2009

Would You Get a Baccalauréat if You Were a Student in France?

French high school students must obtain the baccalauréat if they are to have any chance of getting into university. Almost all teenagers have to write the nationwide standardized tests at the same time. About half of them pass.

Everyone has to write the philosophy exam, which was held yesterday. Charles Bremner tells us what questions were on the exam [Stress test for France's young philosophers]. You have four hours to answer one of the questions. How would you do?
If you were in the economics and social science stream, the questions were ....
  1. What is gained by exchange?
  2. Does technological development transform mankind?
If you were one of the science students the questions were ....
  1. Is it absurd to desire the impossible?
  2. Are there questions which no science can answer?
If you were in the literature stream the questions were ....
  1. Does objectivity in history suppose impartiality in the historian?
  2. Does language betray thought?
To me the questions indicate that France expects more of its potential university students than we do in Canada. We used to have standardized province-wide exams in Ontario but they were abolished 40 years ago. As far as I know we never had a test that everyone in the entire country had to write.

I don't think such a test has ever been popular in the USA.

[Hat Tip: Uncertain Principles: Answers Matter More than Questions]

Deciphering Michael Ruse

To put it mildly, I'm not a big fan of Michael Ruse. I don't think he understands evolution very well in spite of the fact that he gives talks about it all over the world. I've been at some of those talks and they make me very angry [Michael Ruse: 90% 0f Scientists Are Selectionists, Evolution at Chautauqua, Darwinism at the ROM].

Ruse frequently argues the accommodationist position and he's gotten himself in trouble recently by taking on Jerry Coyne [Brown + Ruse vs. Myers: Are atheists responsible for creationism?]. Jason Rosenhouse has weighed in to defend the atheist position, pointing out that Ruse is very confusing [Ruse News]. Sometimes Ruse seems to be aiding and abetting creationism by allying himself with people like Bill Dembski.

Jason is particularly upset by the book Debating Design co-edited by Michael Ruse and Bill Dembski. I'm not bothered so much by this book. In fact, it's a very useful collection of essays by proponents of both sides. That includes people like Francisco Ayala, Ken Miller, Elliott Sober, and Robert T. Pennock.1

In that book, Michael Ruse has an essay on the history of the argument from design. In order to illustrate how inconsistent and frustrating Ruse can be, I've selected a passage from the conclusion to that essay. Here, Ruse seems to be saying that the accommodationists are wrong. I think Ruse has it right, for once.
I draw to the end of my survey of twenty-five hundred years of the argument from design. Deliberately, I have tried to be nonjudgmental, merely telling the story of the ideas as they appear in history. But, as I conclude, I cannot resist drawing an obvious inference from my history. Intelligent Design theorists and atheistical Darwinians cannot both be right, but they are both surely right in thinking that they are more in tune with modern evolutionary biology than are the mainstream reconcilers of science and religion.

1. I agree with Jason when he says, "Making matters worse was the fact that the four essays Ruse chose to represent “Darwinism” added up to a very weak case for the good guys. If all I knew about this issue came from that book, I would be an ID proponent."

Wednesday, June 17, 2009

The Logic (and Intelligence) of Believers

PZ Myers discovered a wonderful website that proves, once again, that the correlation between believers and idiots is very strong and the fight really is between superstition and rationalism.

Have fun at Proof That God Exists.

On Faith and Science

Peter Hess is Faith Project Director at National Center for Science Education (NCSE). (I don't know if they have another director for people who don't rely on faith. Is there an Rationalism Project Director?) Hess was written an article in The Washington Post [On Faith].

It's a typical accommodationist article—full of unsubstantiated statements with no attempt whatsoever to come to grips with the main problem. The article maintains that science and religion are compatible without explaining what kind of religion you have to believe in to avoid conflict with science. Can you believe in miracles, the power of prayer, the existence of a soul, the importance of the Bible, the divinity of Jesus, and life after death without coming into conflict with science?

Joshua Rosenau likes the article by Hess. Josh has posted excerpts on his blog Thoughts from Kansas [NCSE's Peter Hess takes down Disco.'s John West]. Here's one of the excerpts that Josh posted.
Too often, debates over the public perception of evolution are dominated by the fringes, by fundamentalist Christians and others who reject basic science due to their literal reading of the Bible and by ardent atheists who reject religion because they've embraced metaphysical naturalism ― that nature is all that exists. But the silent majority ― that spans the spectrum from theism to atheism ― have no problem reconciling their religious beliefs with established sciences such as evolution, or with new sciences such as stem cell research. My work at the National Center for Science Education brings me into contact with voices across that spectrum and I've found that honest, open, and inclusive dialog is not only possible, but vital for our children's education, for the credibility of religious traditions, and for the continued role of the United States as a scientific and moral leader in our increasingly interconnected world.
There are several problems with the logic expressed here. I'm always suspicious of those who claim to represent the "silent majority" but in this case the claim makes no sense because I'm not convinced that this so-called "silent majority" in the USA actually exists. Is it true that a majority of Americans have "no problem reconciling their religious beliefs with established sciences"?

Now let's imagine a hypothetical situation where Peter Hess is writing an article for a Swedish newspaper, where a majority of citizens are non-religious and atheists could not be labeled a "fringe" group. Would his argument be any weaker because he can no longer claim to represent the "silent majority"? If the answer is "yes" then the argument has no meaning. It's just empty rhetoric. I hate arguments based on the appeal to popularity even if the appeal is merely implicit.

Like Peter Hess, I also value "honest, open and inclusive dialog." That's why I think it's important to debate the conflict between science and religion. If one is being open and honest than one will address the potential sources of conflict such as the existence of a personal god and whether humans have a purpose. It would be dishonest to avoid those issues—and the ones listed above—in order to try and makes religious people more comfortable. It would not be "inclusive" to dismiss atheists as a "fringe" group whose opinions don't count because they're not part of the "silent majority.".

If we really value the education of our children then lets talk about the existence of supernatural beings and let's hear a defense of their existence and not just rhetoric about how belief is the majority position in the USA. Let's hear about those religious traditions that are compatible with science and let's, at least, get rid of the ones that are clearly incompatible.

Finally, who appointed the USA as the "moral leader" of the world? Did I miss the vote?

Tuesday, June 16, 2009

Preparing for Professor Palazzo

Alex Palazzo (The Daily Transcript) is coming to Toronto. In two weeks he will be joining my Department as a Professor (Assistant variety) and colleague.

There's been a flurry of activity in the lab that's been assigned to him. It's just around the corner from my office so I've been able to keep track of the clean-out and the renovations. So far it looks like it will be ready just in time.

It will be exciting to have another blogger in the department. (We already have several.) I'm really looking forward to Alex's arrival so I can teach him a few things about science—things he seems to have missed while doing his post-doc in one of the lesser schools south of the border.

I'm not looking forward to paying off my bet with him. I'd explain why I lost but it's a long story.

Nicholas Wade on the Origin of Life

Nicholas Wade is a science journalist who writes for the New York Times. His particular area of expertise is evolution and molecular biology and he is often mentioned as one of the best science writers in America.

That's not an opinion that I share, although it's true that he writes very well.

Wade's latest article is New Glimpses of Life’s Puzzling Origins. The focus of this article is on recent discoveries in chemistry and biology relating to the origin of life. These all support a scenario where complex molecules in a warm little pond give rise to replicating nucleic acids enclosed in a membrane vesicle. Not much attention is paid to the competing scenarios—especially the one I favor: Metabolism First and the Origin of Life.

Now don't get me wrong. There's no reason why Nicholas Wade can't prefer one particular scenario for the origin of life. After all, many scientists agree with him. The problem I have is that when it comes to informing those who read newspapers, they won't be getting the full story.

One of the "problems" in origin of life studies is the "chirality" problem. The idea is to explain why life prefers left-handed amino acids instead of right-handed amino acids. The "problem" arises when you postulate that life arose in a soup consisting of equal amounts of both types of amino acid.

Sandwalk readers will know my opinion on the "problem." I think it's a "non-problem" since life probably didn't arise from a pool of 20 different concentrated amino acids. I prefer a scenario where a few simple amino acids contributed to the first catalysts and expansion of the repertoire of amino acids resulted from synthesis of more complex ones from simple ones. Since this was "biological" synthesis, the complex amino acids were all left-handed forms from the beginning because the precursors were already left-handed [Can watery asteroids explain why life is 'left-handed'?].

Let's see how Nicholas Wade describes recent results.
Another striking advance has come from new studies of the handedness of molecules. Some chemicals, like the amino acids of which proteins are made, exist in two mirror-image forms, much like the left and right hand. In most naturally occurring conditions they are found in roughly equal mixtures of the two forms. But in a living cell all amino acids are left-handed, and all sugars and nucleotides are right-handed.

Prebiotic chemists have long been at a loss to explain how the first living systems could have extracted just one kind of the handed chemicals from the mixtures on the early Earth. Left-handed nucleotides are a poison because they prevent right-handed nucleotides linking up in a chain to form nucleic acids like RNA or DNA. Dr. Joyce refers to the problem as “original syn,” referring to the chemist’s terms syn and anti for the structures in the handed forms.

The chemists have now been granted an unexpected absolution from their original syn problem. Researchers like Donna Blackmond of Imperial College London have discovered that a mixture of left-handed and right-handed molecules can be converted to just one form by cycles of freezing and melting.
Hmmm ... I see two problems here. First, I'm not aware of any experiments by Donna Blackmond or anyone else that solves the chirality problem. Does anyone have a reference?

The second problem with Wade's description concerns the "handedness" of nucleotides. It's true that the sugar component of nucleotides is exclusively D-ribose (or D-deoxyribose) and not L-ribose. The nucleic acids that we know today (DNA and RNA) could not be made with L-ribose or L-deoxyribose. This is a "problem" that's similar to the one with amino acids; how do you get a pool of sugars that are all D- configurations? (Do you get them by synthesizing them all from D-glyceraldehyde?)

The terms syn and anti refer to different conformations of nucleotides and not different stereoisomers. Conformations are different three-dimensional shapes that a molecule can adopt in solution. They don't require the breaking of any chemical bonds. See Nucleotides Can Adopt Many Different Conformations for a discussion of these different shapes.

Here's a figure showing the anti and syn conformations of deoxyguanylate. (Click to embiggen.)

Free nucleotides can easily switch back and forth between the two forms since all it requires is rotation around the β-N-glycosidic bond—the one with the circular arrow around it. This has nothing to do with stereochemistry or the chirality problem.

In fact, nucleotides like deoxyguanylate can switch between the two conformations even while they are part of DNA. The anti conformation is found in normal B-DNA but the double helix can adopt a Z-DNA conformation under some circumstances and in that conformation the deoxyguanylate residues are in the syn conformation.

Mistakes like this are what makes science journalism difficult. I don't expect Nicholas Wade to be an expert in biochemistry—although if he'd had a copy of my textbook he could have avoided the error. What I do expect is a bit of fact-checking with other experts. Wade could have asked any biochemist to check this out.

Furthermore, Wade should probably have been suspicious when he realized that the syn and anti conformations of nucleotides don't come up in any other discussions about chirality. Indeed, nucleotides are rarely mentioned in such discussions.

[Figure is from Moran/Scrimgeour et al. Biochemistry 2nd ed. (1994) ©Neil Patterson Publishers/Prentice Hall.

Nobel Laureate: Robert Koch


The Nobel Prize in Physiology or Medicine 1905

"for his investigations and discoveries in relation to tuberculosis"

Robert Koch (1843 - 1910) won the Noble Prize in 1905 for demonstrating that specific bacteria can cause common diseases. Tuberculosis was the specific disease mentioned in the citation.

At the time of the award, Koch was already a very famous scientist. Part of his reputation was based on The Most Famous Speech in Medical History but he was also widely respected for identifying the bacteria causes of other diseases.

The most important part of the Presentation Speech is the part that emphasizes the general contribution of Koch to the study of bacteriology (see below). Koch is recognized as one of the founders of the modern field of microbiology. One of his co-workers, Paul Ehrlich, won the Nobel Prize three years after Koch [Nobel Laureate: Paul Ehrlich].
Nobel Laureates
To start with, developing a general methodology is as valuable as finding the correct technique for every special case. Koch's genius has blazed new trails in this respect and has given present-day research its form. To give a detailed description of this is beyond the scope of this account. I only want to mention that he had moreover already given a significant development to techniques in staining and microscopic investigation as well as in the field of experiment in his earliest work. Shortly after this he produced the important method, which is still generally the usual one, of spreading the material under investigation in a solid nutrient medium to allow each individual among the micro-organisms present to develop into a fixed colony, from which it is possible, in further research, to go on to obtain what is known as a pure culture.

Shortly after the publication of his investigations into diseases from wound infections Koch was appointed to the new Institution, the «Gesundheitsamt» (Department of Health), in Berlin. There he started work on some of the most important human diseases, namely, tuberculosis, diphtheria and typhus. He worked on the former one himself. The two latter investigations he left to his first two pupils and assistants, Loeffler and Gaffky. For all three diseases the specific bacteria were discovered and studied in detail.

To give an account of the work which Koch carried out, or accomplished through his pupils, and also to mention the work which derives more indirectly from Koch, would nearly be the same as describing the development of bacteriology over the last few decades. I will content myself with naming some of the most important discoveries and items of research which, in addition to those already named, are more directly linked with Koch's name. At the head of the German Cholera Commission Koch investigated the parasitic aetiology of cholera in Egypt and India, and discovered the cholera bacillus and the conditions necessary for its life. Experience thus gained found practical application in the development of measures taken to prevent and combat this devastating disease. In addition Koch made important investigations concerning plague in humans, malaria, tropical dysentery, and the Egyptian eye disease (trachoma) among others, and now finally concerning typhus recurrens in tropical Africa. He has also carried out work of exceptional importance, concerning a host of destructive tropical cattle diseases, such as rinderpest, Surra disease, Texas fever, and finally concerning coast fever in cattle and the trypanosome disease carried by the tsetse fly.

Through the perfection he gave to methods of culturing and identifying micro-organisms, he has been able to carry out his work with regard to disinfectants and methods of disinfection so important for practical hygiene, and advice concerning the early detection and combating of certain epidemic diseases such as cholera, typhus and malaria.

[Image Credits: photograph:zgapa.pl/drawing: Wolsztyn - Wollstein/statue: Wikipedia/movie poster: Journal of Medicine and Movies]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Monday's Molecule #126: Winner

The molecules are: BMPR = Bone morphogenic bone receptor; BMP4 = Bone morphogenetic protein 4, CHD = Chordin, TGS = twisted gastrulation. These molecules play an important role in regulating development in the embryos of the amphibian (frog) Xenopus laevis.

BMP binds to its receptor (BMPR) on certain cells and acts as a signal leading to induction of a number of developmental genes. Most of them are involved in establishing dorsal-ventral polarity (the back and belly of the the tadpole). Chordin is an antagonist of BMP4 and it is secreted by another group of cells in the early embryo to inhibit the action of BMP4.

The discovery of specific cells that secreted morhogenic factors is mostly due to the pioneering work of Hans Spemann, who was awarded a Nobel Prize in 1935. This marked a turning point in the history of developmental biology because it signaled the transition from a descriptive science to an experimental/molecular/genetic science.

We have a single winner this week. It's Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

Today's molecule is actually four molecules. Your task is to identify the four molecules shown in the cartoon. Explain what they are doing in the figure. Be sure to name the species or you won't get credit for a correct answer.

These molecules are directly connected to one of the most significant Nobel Prizes in the 20th century. The Nobel Laureate didn't know the names of these molecules but that doesn't diminish the achievement. Identify the Nobel Laureate and the connection between Monday's Molecules and the work for which the prize was awarded.

The first person to identify all four molecules and the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for six weeks from the time they first won the prize. Please note the change in the length of time you are ineligible. The idea is to give more more people a chance to win.

There are eight ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, and Bill Chaney of the University of Nebraska.

Bill Chaney has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are allowed.

[Image Credit: De Robertis, E.M. and Kuroda, H. (2004)]

Monday, June 15, 2009

Creationism, ID and the Douchebaggery of Really Bad Arguments: An Evening with the Canadian Cynic

Join us at the Centre for Inquiry (Toronto) for Creationism, ID and the Douchebaggery of Really Bad Arguments: An Evening with the Canadian Cynic.

Sandwalk readers will be able to withstand the suspense since you already know who Canadian Cynic is.

Starts: Friday, July 3rd 2009 at 7:00 pm
Ends: Friday, July 3rd 2009 at 9:00 pm
Location: Centre for Inquiry Ontario, 216 Beverley St., Toronto

Creation Science, Intelligent Design and the Douchebaggery of Really, Really Bad Arguments

A polemic by the Canadian Cynic, aka ???

For over five years, the blogger "Canadian Cynic" has railed against the appalling idiocy of the right-wing wankersphere. Along with his carefully-acquired co-bloggers "LuLu" and "Pretty Shaved Ape", "CC" (as he is known to his readers) has struck fear into the hearts of Canada's wanks from coast to coast, using a combination of awesome intellect, devastating logic and, sometimes, just calling people "douchebags" when the situation calls for it.

And for the first time, he comes out publicly ... at the Centre for Inquiry.

The evening's presentation will consist of some war stories from many years back during CC's anti-creation science years, plus some updates on how, depressingly, nothing seems to have changed.

There will be a subsequent Q/A session, during which outraged audience members will be allowed to vent until told to put a sock in it, after which we will adjourn to a convenient pub that serves real beer, and you're buying.

Event admission: $5 regular, $4 student, FREE for Centre for Inquiry Friends of the Centre

Gene Evolution Process Discovered

This press release heralds a major breakthrough in evolution: Gene Evolution Process Discovered.
One of the mechanisms governing how our physical features and behavioural traits have evolved over centuries has been discovered by researchers at the University of Leeds.

Darwin proposed that such traits are passed from a parent to their offspring, with natural selection favouring those that give the greatest advantage for survival, but did not have a scientific explanation for this process.

In research published this week, the Leeds team reports that a protein known as REST plays a central role in switching specific genes on and off, thereby determining how specific traits develop in offspring.
The article is by Johnson et al. (2009). Here's the abstract.
Specific wiring of gene-regulatory networks is likely to underlie much of the phenotypic difference between species, but the extent of lineage-specific regulatory architecture remains poorly understood. The essential vertebrate transcriptional repressor REST (RE1-Silencing Transcription Factor) targets many neural genes during development of the preimplantation embryo and the central nervous system, through its cognate DNA motif, the RE1 (Repressor Element 1). Here we present a comparative genomic analysis of REST recruitment in multiple species by integrating both sequence and experimental data. We use an accurate, experimentally validated Position-Specific Scoring Matrix method to identify REST binding sites in multiply aligned vertebrate genomes, allowing us to infer the evolutionary origin of each of 1,298 human RE1 elements. We validate these findings using experimental data of REST binding across the whole genomes of human and mouse. We show that one-third of human RE1s are unique to primates: These sites recruit REST in vivo, target neural genes, and are under purifying evolutionary selection. We observe a consistent and significant trend for more ancient RE1s to have higher affinity for REST than lineage-specific sites and to be more proximal to target genes. Our results lead us to propose a model where new transcription factor binding sites are constantly generated throughout the genome; thereafter, refinement of their sequence and location consolidates this remodeling of networks governing neural gene regulation.
Correct me if I'm wrong, but haven't there been occasional rumors about other regulatory proteins (repressors and activators) that might play a role in regulating development? Haven't they sometimes been implicated in causing the differences between species? I seem to remember hearing something about "evo-devo"—does that ring any bells?

Do scientists have any responsibility to make sure their work is accurately reported by university press offices? I think they do.

Johnson, R., Samuel, J., Ng, C.K., Jauch, R., Stanton, L.W., and Wood, I.C. (2009) Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST. Molecular Biology and Evolution 26:1491-1507. [doi:10.1093/molbev/msp058]

Science Scouts

Join Science Scouts and win cool badges! In case you don't know, the complete offical name of Science Scouts is "Order of the Science Scouts of Exemplary Repute and Above Average Physique." (They're lenient about the physique.)

This is one of my favorite badges. All you have to do is Science with no conceivable application (known among friends as the "useless" badge). I've done lots of that kind of science. I'm also eligible for the next level badge— for science that not only has no conceivable application but also isn't even interesting to fellow scientists.

This one's quite ordinary. It's the cloner badge. You can earn it just by cloning something. An advanced version is coming out next year. It's for people who have cloned something that terrorized a small village.

I'm really proud of this one. It's the "somewhat confused as to what scientific field I actually belong to" badge. When you put it on your CV you can refer to it by its more formal name: the transdiscplinary, interdiscplinary, multidisciplinary, or intradisciplinary (TIMI) badge.

Here are some of my other badges ...

[Hat Tip: Eva Amsen]

Who Is Canadian Cynic?

Blogger Canadian Cynic chose to remain anonymous. As most of you know, I prefer bloggers who are not anonymous but I respect the decision of my friends who disagree.

Some of Canadian Cynic's enemies don't respect his decision so they did some digging and outed him. Tsk, tsk, typical behavior for right-wing idiots.

Canadian Cynic is my old friend Rob Day from talk.origins. I'm secretly delighted that he can now be identified even though I deplore the behavior of his enemies.

He's probably going to be giving a talk in Toronto very soon so you can all come out and meet Canadian Cynic [You might want to keep Friday, July 3, open]. I have stories, and lots of photos! So do my daughter Jane and her husband Michael—they rented his house! We'll have a real "outing" party.

BTW, Rob doesn't want anyone to retaliate by outing the right-wing idiots who choose to remain anonymous [On outing].

Canada's Secret Plan for World Domination

The secret is out [Donuts To Dollars].
Our Friendly Neighbors In Canada Are About To Wage An International Food Fight Over Your Morning Coffee

(CBS) Americans are about to be dragged into an international food fight … and it's our friendly neighbors in Canada who are throwing down the gauntlet. Jeff Glor reports our Cover Story:
There was some chance that the story would be ignored since it only appeared on CBS News but that turned out to be a forlorn hope. John Pieret of Thoughts in a Haystack has taken on the role of a modern Paul Revere [Rally 'Round the Flag].

Now the whole world knows the secret.